[R-sig-Debian] updating r-cran- packages on a new Ubuntu lucid system
friendly at yorku.ca
Tue Feb 1 16:56:05 CET 2011
On 1/31/2011 12:14 PM, Dirk Eddelbuettel wrote:
> On 31 January 2011 at 09:04, Michael Friendly wrote:
> | I'm not any further ahead in trying to update vcd from 1.2-7 to 1.2-9.
> | How can I resolve this?
> If what you're doing doesn't work, do something else. The .deb package are
> convenient. They can't all be recent because, well, a distro has release
OK: I used (as sudo)
and it seemed to work; however old.packages() still reports vcd at
1.2-7. Why is that?
Loading required package: MASS
Loading required package: grid
Loading required package: colorspace
R version 2.12.1 (2010-12-16)
Platform: x86_64-pc-linux-gnu (64-bit)
attached base packages:
 grid stats graphics grDevices utils datasets methods
other attached packages:
 vcd_1.2-9 colorspace_1.0-1 MASS_7.3-9
loaded via a namespace (and not attached):
Package LibPath Installed Built ReposVer
rgl "rgl" "/usr/lib/R/site-library" "0.89" "2.10.1" "0.92.798"
vcd "vcd" "/usr/lib/R/site-library" "1.2-7" "2.9.2" "1.2-9"
In addition, some follow up questions, unanswered by reading
/bin/linux/ubuntu/README. I'm persisting
in this because I'm setting up a new system, and want to insure that I
don't create maintenance problems
down the road.
(a) At present, I have access to this machine only via a remote terminal
window; no X11. Is there any way
to install a package like r-cran-rgl that seems to require X11?
(b) It seems to be recommended to maintain the distinction between
r-cran-* packages, which I should install
as root via apt-get and non-r-cran packages, which I should install in
R_LIBS_USER = "~/lib/R/library" as my normal user.
Is this correct?
I'm the only R user on this machine, so it seems simpler to install
*all* packages as root and let them go into
Q: will this cause any problems with apt-get upgrade finding
non-cran-r packages there?
Alternatively, if I try to install non-cran packages via
install.packages() as my normal user,
Q: How to distinguish, in R, r-cran from non-r-cran packages?
Q: How to handle dependencies, where a non-cran package requires an
e.g., in Windows, I would just run the following to install a bunch of
(non-cran) packages, and be done with it.
mypkgs <- c("vcdExtra", "HistData", "candisc", "tableplot", "Guerry",
otherpkgs <-c("ca", "catspec", "coin", "corrgram", "gmodels", "gnm",
"ggplot2", "plyr", "sem")
allpkgs <- union(mypkgs, otherpkgs)
# install the above, along with any dependencies
# update any recently modified packages
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street Web: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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